Metagene plot error!

[Raoyugithub]

Hi, I have met the following problem (see the error code) while running the software. Can you help me out? Thanks! This is the error code: This is the attribute.txt: This is the longest.transcripts.info.txt

[sherkinglee]

Hi, It seems like you installed an older version of RiboMiner. You can update the RiboMiner to version 0.2.3.2 and try it again. But the problem may be the format of your attribute file. Make sure all columns are split by TAB rather than blank space.

Best, Sherking

[Raoyugithub]

Thanks, the attribute file was generated by the script automatically. I will check the attribute file, may also update the software and try again.

[Raoyugithub]

Hi, It seems like you installed an older version of RiboMiner. You can update the RiboMiner to version 0.2.3.2 and try it again. But the problem may be the format of your attribute file. Make sure all columns are split by TAB rather than blank space.

Best, Sherking

I tiired with the following command: MetageneAnalysis -i CK/CK_1Aligned.sortedByCoord.out.bam -c longest.transcripts.info.txt -o test -s 12,13,13 -t CK1 -r 26,27,28

New errors happen again:

![Uploading image.png…]()

[Raoyugithub]

[sherkinglee]

Oh, I am sorry for making you confused! Actually, the bam file you used for metagene analyses here is the genome bam file. However, MetageneAnalysis requires a bam file with transcriptome level. So you need use the _CK1Aligned.toTranscriptome.out.sorted.bam file for this analysis. By the way, have you succeeded with MetageneAnalysisForTheWholeRegions function as you mentioned for the first time?

Hope you will succeed this time!

best wishes, Sherking

[Raoyugithub]

Hi, Sherking: With one bam file, it worked. But with the attribute.txt file, I got a new error:

[sherkinglee]

Hi, I think it is better to present all details about the command and attribute file rather than just your screen plot. For example, the attribute file is like:

bamFiles        readLengths     Offsets bamLegends
ctrl1.Aligned.toTranscriptome.out.sorted.bam  28,29,30     12,12,13       Ctrl-1
treat1.Aligned.toTranscriptome.out.sorted.bam      28,29,30     12,12,13       Treat-1

And the command you used should be (e.g.):

MetageneAnalysisForTheWholeRegions -f attributes.txt -c longest.transcript.info.txt -o test -b 15,90,15 -l 100 -n 10 -m 1 -e 5

In your case here, you should use "-f" parameter rather than "-i" with the attribute file.

Sherking

[Raoyugithub]

Thanks, Now, it works. Many thanks for your kind help!!!

[sherkinglee]

That's great! Enjoy your ribosome profiling data analyses!

[Raoyugithub]

Thanks. Collectively, it might be the attribute file problem, I checked and double-checked the file format many times and make sure they are tabbed, but bugs persisted. Finally, I remade the file from the scratch and issues solved. You are correct, it was the attribute file format issue. Thanks again, Besides, mybe the update of the software also helps. Hope this will help others.